Merge branch 'release-1.31.0'

PavlidisLab · Jan 23, 2024 · 659cabe · 659cabe
2 parents c2d29b4 + 712827f
commit 659cabe
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diff --git a/.editorconfig b/.editorconfig
@@ -1,11 +1,24 @@
 root = true
 
+[Jenkinsfile]
+indent_style=space
+indent_size=4
+
+[init-indices.sql]
+indent_size=2
+
 [/pom.xml]
 indent_style=tab
 
 [/gemma-web/pom.xml]
 indent_style=tab
 
+[BioMaterial.hbm.xml]
+indent_size=3
+
+[BioAssay.hbm.xml]
+indent_size=3
+
 [Investigation.hbm.xml]
 indent_style=tab
 
@@ -25,4 +38,7 @@ indent_size=3
 indent_style=tab
 
 [gemma-web/**/applicationContext-security.xml]
-indent_style=tab
+indent_style=tab
+
+[dwrServices.js]
+indent_size=4
diff --git a/.idea/codeStyles/Project.xml b/.idea/codeStyles/Project.xml
diff --git a/.idea/runConfigurations/Gemma_CLI.xml b/.idea/runConfigurations/Gemma_CLI.xml
diff --git a/.jenkins/Jenkinsfile b/.jenkins/Jenkinsfile
@@ -165,8 +165,8 @@ pipeline {
  }
  steps {
  sh 'mvn -B site-deploy'
- sh "ln -sf ${siteDir}/gemma/gemma-${gemmaVersion} ${dataDir}/gemma-devsite"
- sh "ln -sf ${siteDir}/baseCode/baseCode-${baseCodeVersion} ${dataDir}/basecode-site"
+ sh "ln -Tsf ${siteDir}/gemma/gemma-${gemmaVersion} ${dataDir}/gemma-devsite"
+ sh "ln -Tsf ${siteDir}/baseCode/baseCode-${baseCodeVersion} ${dataDir}/baseCode-site"
  }
  }
  stage ('Deploy Gemma Web') {
@@ -192,7 +192,7 @@ pipeline {
  }
  }
  steps {
- sh "rsync -adv gemma-cli/target/appassembler ${cliDir}"
+ sh "rsync -av --delete gemma-cli/target/appassembler/ ${cliDir}/"
  }
  }
  }

diff --git a/.jenkins/README.md b/.jenkins/README.md
@@ -0,0 +1,8 @@
+This folder contains a configuration for Jenkins and a script to validate the
+Jenkinsfile.
+
+Run the following before pushing any changes to the CI configuration:
+
+```bash
+.jenkins/validate-jenkinsfile
+```
diff --git a/.jenkins/validate-jenkinsfile b/.jenkins/validate-jenkinsfile
@@ -0,0 +1,4 @@
+#!/bin/bash
+JENKINS_URL=https://jenkins.pavlab.msl.ubc.ca
+JENKINS_CRUMB=`curl "$JENKINS_URL/crumbIssuer/api/xml?xpath=concat(//crumbRequestField,\":\",//crumb)"`
+curl -X POST -H $JENKINS_CRUMB -F "jenkinsfile=<$(dirname "${BASH_SOURCE[0]}")/Jenkinsfile" $JENKINS_URL/pipeline-model-converter/validate
diff --git a/gemma-cli/pom.xml b/gemma-cli/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.30.6</version>
+ <version>1.31.0</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-cli</artifactId>

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/AffyDataFromCelCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/AffyDataFromCelCli.java
@@ -22,6 +22,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
 import ubic.gemma.core.loader.expression.DataUpdater;
 import ubic.gemma.core.loader.expression.geo.model.GeoPlatform;
@@ -182,7 +183,7 @@ protected void doWork() throws Exception {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) {
+ protected void processOptions( CommandLine commandLine ) throws ParseException {
  super.processOptions( commandLine );
  if ( commandLine.hasOption( AffyDataFromCelCli.APT_FILE_OPT ) ) {
  this.aptFile = commandLine.getOptionValue( AffyDataFromCelCli.APT_FILE_OPT );

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/AffyProbeCollapseCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/AffyProbeCollapseCli.java
@@ -22,6 +22,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import ubic.gemma.core.analysis.sequence.SequenceManipulation;
 import ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader;
 import ubic.gemma.model.expression.designElement.CompositeSequence;
@@ -69,7 +70,7 @@ protected void buildOptions( Options options ) {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) {
+ protected void processOptions( CommandLine commandLine ) throws ParseException {
  super.processOptions( commandLine );
  affyProbeFileName = commandLine.getOptionValue( "affyProbeFile" );
  }

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAlternativePopulateCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAlternativePopulateCli.java
@@ -24,7 +24,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.core.io.ClassPathResource;
 import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
-import ubic.gemma.core.util.AbstractCLIContextCLI;
+import ubic.gemma.core.util.AbstractAuthenticatedCLI;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 
@@ -38,7 +38,7 @@
  *
  * @author paul
  */
-public class ArrayDesignAlternativePopulateCli extends AbstractCLIContextCLI {
+public class ArrayDesignAlternativePopulateCli extends AbstractAuthenticatedCLI {
 
  @Override
  public CommandGroup getCommandGroup() {
@@ -61,7 +61,7 @@ protected boolean requireLogin() {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) throws Exception {
+ protected void processOptions( CommandLine commandLine ) {
 
  }
 

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAnnotationFileCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAnnotationFileCli.java
@@ -18,21 +18,11 @@
  */
 package ubic.gemma.core.apps;
 
-import java.io.BufferedReader;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
-
 import ubic.gemma.core.analysis.service.ArrayDesignAnnotationService;
 import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
 import ubic.gemma.core.genome.gene.service.GeneService;
@@ -45,6 +35,11 @@
 import ubic.gemma.model.genome.Taxon;
 import ubic.gemma.persistence.service.genome.taxon.TaxonService;
 
+import java.io.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+
 /**
  * Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for
  * the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or
@@ -107,9 +102,9 @@ protected void buildOptions( Options options ) {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) {
+ protected void processOptions( CommandLine commandLine ) throws ParseException {
 
- if ( autoSeek ) {
+ if ( isAutoSeek() ) {
  throw new IllegalArgumentException( "This CLI doesn't support the auto option" );
  }
 
@@ -333,7 +328,7 @@ private void processFromListInFile() throws IOException {
  continue;
  }
 
- ArrayDesign arrayDesign = this.locateArrayDesign( accession, getArrayDesignService() );
+ ArrayDesign arrayDesign = this.locateArrayDesign( accession );
 
  try {
  this.processAD( arrayDesign );

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBioSequenceDetachCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBioSequenceDetachCli.java
@@ -21,8 +21,8 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent;
-import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.expression.designElement.CompositeSequence;
 import ubic.gemma.model.genome.biosequence.BioSequence;
@@ -61,7 +61,7 @@ protected void buildOptions( Options options ) {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) {
+ protected void processOptions( CommandLine commandLine ) throws ParseException {
  super.processOptions( commandLine );
  this.delete = commandLine.hasOption( "delete" );
  }

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBlatCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBlatCli.java
@@ -21,6 +21,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
 import ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService;
 import ubic.gemma.core.loader.genome.BlatResultParser;
@@ -36,7 +37,7 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Date;
-import java.util.concurrent.*;
+import java.util.concurrent.Callable;
 
 /**
  * Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB. You must
@@ -72,6 +73,7 @@ protected void buildOptions( Options options ) {
  .desc(
  "Threshold (0-1.0) for acceptance of BLAT alignments [Default = " + this.blatScoreThreshold + "]" )
  .longOpt( "scoreThresh" )
+ .type( Double.class )
  .build();
 
  options.addOption( Option.builder( "sensitive" ).desc( "Run on more sensitive server, if available" ).build() );
@@ -89,7 +91,7 @@ protected void buildOptions( Options options ) {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) {
+ protected void processOptions( CommandLine commandLine ) throws ParseException {
  super.processOptions( commandLine );
 
  if ( commandLine.hasOption( "sensitive" ) ) {
@@ -105,7 +107,7 @@ protected void processOptions( CommandLine commandLine ) {
 // }
 
  if ( commandLine.hasOption( 's' ) ) {
- this.blatScoreThreshold = this.getDoubleOptionValue( commandLine, 's' );
+ this.blatScoreThreshold = ( Double ) commandLine.getParsedOptionValue( 's' );
  }
 
  TaxonService taxonService = this.getBean( TaxonService.class );

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignMergeCli.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignMergeCli.java
@@ -21,6 +21,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
 import ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
@@ -95,14 +96,14 @@ protected void buildOptions( Options options ) {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) {
+ protected void processOptions( CommandLine commandLine ) throws ParseException {
  super.processOptions( commandLine );
  if ( commandLine.hasOption( 'o' ) ) {// required
  String otherArrayDesignName = commandLine.getOptionValue( 'o' );
  String[] names = StringUtils.split( otherArrayDesignName, ',' );
  this.otherArrayDesigns = new HashSet<>();
  for ( String string : names ) {
- ArrayDesign o = this.locateArrayDesign( string, getArrayDesignService() );
+ ArrayDesign o = this.locateArrayDesign( string );
  if ( o == null ) {
  throw new IllegalArgumentException( "Array design " + string + " not found" );
  }

diff --git a/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignProbeCleanupCLI.java b/gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignProbeCleanupCLI.java
@@ -21,9 +21,9 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
 import ubic.gemma.core.util.AbstractCLI;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.expression.designElement.CompositeSequence;
@@ -38,7 +38,6 @@
  *
  * @author Paul
  */
-@Component
 public class ArrayDesignProbeCleanupCLI extends ArrayDesignSequenceManipulatingCli {
 
  @Autowired
@@ -59,7 +58,7 @@ protected void buildOptions( Options options ) {
  }
 
  @Override
- protected void processOptions( CommandLine commandLine ) {
+ protected void processOptions( CommandLine commandLine ) throws ParseException {
  super.processOptions( commandLine );
  if ( commandLine.hasOption( 'f' ) ) {
  file = commandLine.getOptionValue( 'f' );